Supramolecular Assembly and Interfacial Hydration of Tandem Repeat Dipeptides on 2D Nanomaterials: Insights From 3D‐AFM Measurements and MD Simulations

The design of functional bionanomaterials formed by peptide supramolecular organizations on atomically-thick solids relies on understanding molecular self-assembly mechanisms. This study investigates the structural aspects of short peptide assemblies on 2D crystallographic solid surfaces, aiming to create structurally well-defined peptide-solid hybrid systems with soft interfaces. The understanding of complex interplay between sequence-specific molecular interactions among peptides and substrates toward controlled nanoarchitecture formation remains challenging. The lack of understanding of the role of local hydration structures at the molecular level further hinders the rational design and functional control of these systems. A custom-built atomic force microscope, complemented by molecular dynamics simulations, is used to study the assembly of Tyr-His (YH) dipeptides with tandem repeats on cleaved graphite and MoS₂ substrates. Molecular visualization of assembled peptide nanostructures and associated localized 3D hydration structures in aqueous solutions demonstrates that the peptides form fully extended, linear conformations aligned with specific crystallographic orientations on the solid substrate. The physical lengths of the assembled peptides match their unfolded states, including the hydration layers. These results underscore the critical role of water in stabilizing and organizing peptide assemblies on solid substrates. This bio/nano system with well-controlled nanoarchitecture offers a highly potent biofunctionalization platform for biomedical and bionanotechnology applications, such as biosensors and bioelectronics.